I found the cause, mysql user has no permissions for mysql/data folder, I set as the owner and MySQL start without much problems, it's still throwing the other log warning but I cannot see any problem around that, it's not affecting the start up.

Can you run these commands to check the permission of these files? According to the last line in the log file '/etc/gonit/gonitrc' must be owned by you. the issue could be related to this. You can check it running